BAM mapped and unmapped files to fq.gz paired-end reads

Question

[Lissa Cruz Saavedra]

I would like to know if I could merge mapped and unmapped files to generate fq.gz paired-end reads and If the last one has the same content as the original fq.gz file that I used to make the alignment.

[GenoMax]

You should check if the aligned BAM files you have contain unmapped reads. If it does then you just need that file to re-generate the paired-end fastq reads that went into the alignment.

[Lissa Cruz Saavedra]

I am sorry if I don't have too much experience using bioinformatic tools but I would like to make the following question. I used BWA to make the alignment, I know I can get unmapped reads from my bam output, that means the output file contains both kind of reads (mapped and unmapped), right?

Thank you so much for your answer!

[GenoMax]

If you are able to get unmapped reads from your BAM file (e.g. with A: How To Filter Mapped Reads With Samtools ) then yes. Unmapped reads will have a * in column number 3 in your BAM file (check with samtools view your.bam | head -30).

[Lissa Cruz Saavedra]

Thank you for all of your help!.

Just last question. I applied some filters on first bam output, sorted, realignment and markduplicates. Should I use the first bam output or could I use the bam with all those filters?